Integrating single-nucleus transcriptome and GWAS reveals AhTGA1 regulating hypocotyl development in peanut

Highlights 1 Constructed a high-resolution transcriptomic atlas of peanut hypocotyls, identifying 6 major cell types and their developmental trajectories. Integrated snRNA-seq and GWAS to identify AhTGA1 as the key gene regulating hypocotyl length. Demonstrated that AhTGA1 promotes hypocotyl elongation by activating the auxin pathway. Peanut hypocotyl connects the root system and cotyledons, acting as a crucial conduit for transporting nutrients and signaling molecule transport during seedling emergence. Despite its importance, gene expression at the cellular level in peanut hypocotyls has not been characterized. In this study, we created a single nucleus transcriptome atlas for peanut hypocotyls by profiling nearly 29,915 nuclei identifying six major cell types. Pseudotemporal analysis showed a hierarchical differentiation path from progenitor primordium cells to specialize stele cells. By integrating these data with bulk RNA-seq, we found 93 core differentially expressed genes (core-DEGs), including 21 transcription factors (TFs) enriched in phloem and cambium cells. Coexpression network analysis revealed functional modules associated with photosynthesis and fatty acid metabolism. A genome wide association study of hypocotyl length in a diverse peanut panel pinpointed a key locus on chromosome B03 containing the nucleus localization bZIP transcription factor gene AhTGA1 . Expression analysis showed that accessions with high AhTGA1 expression like R169 material exhibited significantly elongated hypocotyls as compared to the accessions with lower high AhTGA1 expression. Further overexpression of AhTGA1 in Arabidopsis obviously promoted the hypocotyl elongated faster than wild-type by activating the auxin pathway. This work provides single-nucleus resolution insights into transcription regulation in hypocotyl development and identifies AhTGA1 as a critical regulator, and offering molecular targets for next precision peanut seedlings breeding with moderate hypocotyl length.